tbuckley/cabot-search huggingface dataset:
Efficacy of bile salt hydrolase synthesizing probiotic bacteria in the treatment of irritable bowel syndrome with diarrhea
Authors: S.P. Polishchuk, A.V. Neverovskyi
Journal: GASTROENTEROLOGY (2023)

Background. One of the mechanisms of the of irritable bowel syndrome with diarrhea (IBS-D) is bile acid malabsorption (BAM). In addition to the use of bile acid sequestrants, probiotic bacteria synthesizing bile salt hydrolase (BSH) are promising in the treatment of probable BAM. The purpose of the study was to compare the effectiveness of combined treatment (a probiotic based on strains of Lactobacillus, Streptococcus, Bifidobacterium, Saccharomyces boulardii and cholestyramine) with cholestyramine monotherapy in the treatment of IBS-D. Materials and methods. A 12-week randomized study included 108 patients with IBS-D divided into a control group (n = 51) receiving only cholestyra­mine and an experimental group (n = 57) receiving a combination of cholestyramine and the study probiotic. At baseline, the relative activity of BSH of the study probiotic capsules was determined. During the stages of the study, patients were examined using clinical scales. Results. The relative activity of BSH of the capsules with the studied probiotic was (2.07 ± 0.06) U/ml compared to (1.00 ± 0.04) U/ml of capsules with L.plantarum and (0.03 ± 0.01) U/ml — with L.plantarum without BSH genes. In the experimental group, the severity of bloating and visceral sensitivity index were lower after 8 and 12 weeks, and the value of the stool type according to the Bristol scale and its daily frequency — after 12 weeks compared to the control group, p &lt; 0.05. According to the scale of IBS-adequate relief, the percentage of achieving a clinical effect was higher in the experimental group compared to the controls after 12 weeks, odds ratio was 1.31 (95% confidence interval 1.03–1.68), p = 0.038. Conclusions. Additional prescription of a probiotic with BSH synthesizing bacterial strains is more effective in improving clinical manifestations of IBS-D and achieving a therapeutic effect compared to cholestyramine monotherapy.
Trends in Laboratory-Confirmed SARS-CoV-2 Reinfections and Associated Hospitalizations and Deaths Among Adults Aged ≥18 Years — 18 U.S. Jurisdictions, September 2021–December 2022
Authors: Kevin C. Ma, Vajeera Dorabawila, Tomás M. León, Hannah Henry, Amelia G. Johnson, Eli Rosenberg, Joshua A. Mansfield, Claire M. Midgley, Ian D. Plumb, Julia Aiken, Quratul Ain Khanani, Steven Auche, Nagla S. Bayoumi, Sarah A. Bennett, Carmen Bernu, Carolyn Chang, Kathryn J. Como-Sabetti, Kevin Cueto, Spencer Cunningham, Meredith Eddy, Rebecca A. Falender, Aaron Fleischauer, Darren M. Frank, Pauline Harrington, Mikhail Hoskins, Adam Howsare, Lucy M. Ingaiza, Aras S. Islam, Shelli A. Jensen, Jefferson M. Jones, Grace Kambach, FNU Kanishka, Yuriy Levin, John F. Masarik, Stephanie D. Meyer, Lauren Milroy, Keeley J. Morris, John Olmstead, Nina S. Olsen, Enaholo Omoike, Komal Patel, Amanda Pettinger, Melissa A. Pike, Isaiah G. Reed, Elizabeth Slocum, Melissa Sutton, Buddhi P. Tilakaratne, Hailey Vest, Johanna Vostok, Jennifer S. Wang, Lydia Watson-Lewis, Haley N. Wienkes, Melissa Briggs Hagen, Benjamin J. Silk, Heather M. Scobie
Journal: MMWR Morbidity and Mortality Weekly Report (2023)

Although reinfections with SARS-CoV-2 have occurred in the United States with increasing frequency, U.S. epidemiologic trends in reinfections and associated severe outcomes have not been characterized. Weekly counts of SARS-CoV-2 reinfections, total infections, and associated hospitalizations and deaths reported by 18 U.S. jurisdictions during September 5, 2021-December 31, 2022, were analyzed overall, by age group, and by five periods of SARS-CoV-2 variant predominance (Delta and Omicron [BA.1, BA.2, BA.4/BA.5, and BQ.1/BQ.1.1]). Among reported reinfections, weekly trends in the median intervals between infections and frequencies of predominant variants during previous infections were calculated. As a percentage of all infections, reinfections increased substantially from the Delta (2.7%) to the Omicron BQ.1/BQ.1.1 (28.8%) periods; during the same periods, increases in the percentages of reinfections among COVID-19-associated hospitalizations (from 1.9% [Delta] to 17.0% [Omicron BQ.1/BQ.1.1]) and deaths (from 1.2% [Delta] to 12.3% [Omicron BQ.1/BQ.1.1]) were also substantial. Percentages of all COVID-19 cases, hospitalizations, and deaths that were reinfections were consistently higher across variant periods among adults aged 18-49 years compared with those among adults aged ≥50 years. The median interval between infections ranged from 269 to 411 days by week, with a steep decline at the start of the BA.4/BA.5 period, when >50% of reinfections occurred among persons previously infected during the Alpha variant period or later. To prevent severe COVID-19 outcomes, including those following reinfection, CDC recommends staying up to date with COVID-19 vaccination and receiving timely antiviral treatments, when eligible.
The influence of hormonal status on the hepatotropic effect and metronidazole in chronic liver damage and the administration of placenta cryoextract
Authors: I.V. Koshurba, F.V. Hladkykh, M.O. Chyzh
Journal: GASTROENTEROLOGY (2023)

Background. Liver diseases occupy an important place in the structure of gastrointestinal pathology and remain an important medical and social problem throughout the world. Almost half of patients with manifest disorders of the hepatobiliary system have a polymorbid status or a high risk of developing concomitant pathology. One of the variants of the combined pathology in the clinic of gastroenterology is peptic ulcer on the background of liver disorders. As a potential anti-ulcer biotechnological agent with a hepatoprotective effect, cryocell — placenta cryoextract, a domestic drug, attracted attention. The purpose was to determine the gender aspects of the hepatotropic effect of placenta cryoextract in tetrachloromethane hepatitis with background ethanol-induced liver cirrhosis and liver damage by antiulcer agents. Materials and methods. Hepatotropic effects were studied at different levels of sex hormones in 112 male and female rats weighing 200–220 g, divided into 4 groups of 28 animals each. Tetrachloromethane hepatitis with background ethanol-induced liver cirrhosis was simulated by administration of an oily solution of tetrachloromethane in combination with a 5.0% ethanol solution for 45 days. Modulation of the content of sex hormones was achieved by surgical ovariectomy or orchiectomy. The activity of γ-glutamyl-transpeptidase was determined by the spectrophotometric method according to G. Szasz.
Сonnection of immunological markers with morphological manifestations in ulcerative colitis
Authors: M.V. Stoikevych, Yu.A. Gaydar, O.M. Tatarchuk, D.F. Mylostуva, T.S. Tarasova, O.P. Petishko
Journal: GASTROENTEROLOGY (2023)

Background. Inflammatory bowel diseases, including ulcerative colitis and Crohn’s disease, are an urgent problem of modern gastroenterology. Therefore, the discovery of new laboratory approaches makes it possible to assess the degree of the disease. Purpose: to reveal the relationship between morphological manifestations and immunological indicators in patients with ulcerative colitis. Materials and methods. The studies were conducted on biological material (blood and colonic biopsy samples) of 90 patients with ulcerative colitis. The thickness of the mucosa, density of the inflammatory infiltrate and its composition, crypt sizes, their architectonics, the presence of crypt abscesses, atrophic and fibrotic changes were calculated in biopsies by morphological and morphometric methods. Immunological studies included the evaluation of mononuclear cells, the levels of B-lymphocytes, interleukin-10, tumor necrosis factor α, immunoglobulins (Ig) A, M, G. Results. The histological activity of the disease was determined by an increased level of inflammatory infiltrate (14,431.4 ± 483.3 per 1 mm2 of stroma) and the presence of many neutrophilic granulocytes (212.2 ± 20.9 per 1 mm2 of stroma) and lymphocytes (2,922.8 ± 76.6 per 1 mm2 of stroma) in it. Also, some patients had crypt abscesses (36.7 % of the total number of patients) and breaches in the epithelial integrity (54.4 % of the total number of patients). A correlation was found between the level of CD22+ lymphocytes and some morphometric parameters: the width of the crypts (r = 0.27; P &lt; 0.01) and the height of the surface epithelium (r = 0.30; P &lt; 0.01); between IgM concentrations and cellular density of mucosal infiltrate (r = 0.29; P &lt; 0.01), neutrophils (r = 0.28; P &lt; 0.01) and basophils (r = 0.24; P &lt; 0.05); level of IgA and macrophages (r = 0.21; P &lt; 0.05), lymphocytes (r = 0.24; P &lt; 0.05), basophils (r = 0.25; P &lt; 0.05). Conclusions. It is shown that some morphological and morphometric indicators are related to immunological parameters. It was found that the elevated level of cytokines correlates with the activity of inflammation in patients with ulcerative colitis. The level of CD22+ lymphocytes and changes in some morphometric indicators (crypt width and surface epithelium height) are directly related to an increase in inflammatory processes in the intestinal mucosa.
Effectiveness of Up-to-Date COVID-19 Vaccination in Preventing SARS-CoV-2 Infection Among Nursing Home Residents — United States, November 20, 2022–January 8, 2023
Authors: Emily Wong, Kira Barbre, Ryan E. Wiegand, Hannah E. Reses, Heather Dubendris, Megan Wallace, Philip Dollard, Jonathan Edwards, Minn Soe, Lu Meng, Andrea Benin, Jeneita M. Bell
Journal: MMWR Morbidity and Mortality Weekly Report (2023)

Nursing home residents have been disproportionately affected by the COVID-19 pandemic; their age, comorbidities, and exposure to a congregate setting has placed them at high risk for both infection and severe COVID-19-associated outcomes, including death (1). Receipt of a primary COVID-19 mRNA vaccination series (2) and monovalent booster doses (3) have been demonstrated to be effective in reducing COVID-19-related morbidity and mortality in this population. Beginning in October 2022, the National Healthcare Safety Network (NHSN) defined up-to-date vaccination as receipt of a bivalent COVID-19 mRNA vaccine dose or completion of a primary series within the preceding 2 months.* The effectiveness of being up to date with COVID-19 vaccination among nursing home residents in preventing SARS-CoV-2 infection is not known. This analysis used NHSN nursing home COVID-19 data reported during November 20, 2022-January 8, 2023, to describe effectiveness of up-to-date vaccination status (versus not being up to date) against laboratory-confirmed SARS-CoV-2 infection among nursing home residents. Adjusting for calendar week, county-level COVID-19 incidence, county-level social vulnerability index (SVI), and facility-level percentage of staff members who were up to date, up-to-date vaccine effectiveness (VE) against infection was 31.2% (95% CI = 29.1%-33.2%). Nursing home residents should stay up to date with recommended age-appropriate COVID-19 vaccination, which now includes an additional bivalent vaccine dose for moderately or severely immunocompromised adults aged ≥65 years to increase protection against SARS-CoV-2 infection.
Features of the intestinal microbiome in patients with gluten-sensitive diseases who are on a gluten-free diet
Authors: O.Yu. Gubska, A.A. Kuzminets, O.R. Denesyuk, O.K. Koliada, V.V. Moseyko, O.A. Dolko
Journal: GASTROENTEROLOGY (2023)

Background. Intestinal dysbiosis is associated with violating both quantitative and qualitative intestinal microbiome (IM) composition. It accompanies different gastrointestinal disorders, including non-celiac gluten sensitivity (NCGS) and celiac disease (CD). A gluten-free diet is the only existing treatment for CD and NCGS. One of the questions of interest is the characteristics of the IM of patients with gluten-related diseases and its relationship with diet therapy. Materials and methods. The study included 25 adults, 14 (56 %) with CD and 11 (44 %) with NCGS; all were on agliadin diet. We determined the faecal content of the Bacteroidetes, Firmicutes, and Actinobacteria and the rest bacterial DNA (“other” indicator) using the real-time polymerase chain reaction. Results. The Bacteroidetes content was 28.4 (Q1-Q3 9.195–37.83) % in CD and 24.98 (Q1-Q3 9.615–30.597) % in NCGS patients, p = 0.565. Firmicutes content was 53.47 (Q1-Q3 49.98–56.798) % in CD patients and 53.0 (Q1-Q3 48.12–68.53) % in NCGS, p = 0.763. The Actinobacteria content was 4.8 (Q1-Q3 3.82–6.84) % in CD patients and 5.37 (Q1-Q3 4.09–7.77) % in NCGS, p = 0.572. There was a moderate positive correlation with the diet duration (p = 0.397, p = 0.03). The Firmicutes/Bacteroidetes ratio was 1.996 (Q1-Q3 1.35–6.85) in CD patients and 2.0 (Q1-Q3 1.65–7.58) in NCGS patients, p = 0.681. The content of “other” types of IM was 15.39 (Q1-Q3 7.44–22.33) % in CD patients and 13.78 (Q1-Q3 10.65–15.58) % in NCGS patients, p = 0.936. Conclusions. We found similar intestinal microbiome features in patients with celiac disease and non-celiac gluten sensitivity. The detected intestinal microbiome changes are most likely to be a consequence of dietary features in such patients, namely the side effect of maintaining an agliadin diet.
Nature of intestinal microflora disorders in cardiovascular diseases
Authors: Yu.M. Stepanov, I.Ya. Budzak
Journal: GASTROENTEROLOGY (2023)

The article reviews the literature on the relationship between intestinal microflora and cardiometabolic disorders. The pathophysiological significance of microflora disturbance in the development of intestinal pathology has long been known and proven. However, scientific research in recent decades has convincingly proven that the positive role of intestinal microbiota is not limited only to the intestines. Disturbances of the intestinal microbiota can affect other organs and systems, in particular, cardiometabolic processes. The mechanism of the relationship between dysbiotic disorders and the cardiovascular system can occur due to the deterioration of the intestinal barrier function and through the influence of various metabolites of the intestinal microflora on cardiometabolic processes. When the intestinal barrier deteriorates, pro-inflammatory harmful components of the intestinal microflora such as lipopolysaccharides can have a negative effect on the cardiovascular system. Short-chain fatty acids, bile acids, and trimethylamine N-oxide are of the greatest importance among the metabolites of the intestinal microflora, which can have a diverse effect on cardiometabolic processes. Accumulated research data indicate the possible impact of intestinal microflora disturbances on atherosclerosis, hypertension, and chronic heart failure. The search for methods of correcting the intestinal flora is underway, which would allow to eliminate the specified negative impact.
Panteleimon Zuichenko, the author of the memoirs about Dmytro Yavornytskyi
Authors: M.P. Chaban, Z.I. Shevtsova, V.V. Gaponov
Journal: GASTROENTEROLOGY (2023)

The article describes the life and professional path of Panteleimon Zuichenko, an otolaryngologist. His intellectual entourage is represented. Information is provided about the preservation of the original autobiography of the outstanding Ukrainian poet Taras Shevchenko in the Zuichenko family. The presented material will contribute to the popularization of the figure of the Ukrainian zemstvo doctor.
High-plex immunofluorescence imaging and traditional histology of the same tissue section for discovering image-based biomarkers
Authors: Jia-Ren Lin, Yu-An Chen, Daniel Campton, Jeremy Cooper, Shannon Coy, Clarence Yapp, Juliann B Tefft, Erin McCarty, Keith L Ligon, Scott J Rodig, Steven Reese, Tad George, Sandro Santagata, Peter K Sorger
Journal: Nature Cancer (2023)

Precision medicine is critically dependent on better methods for diagnosing and staging disease and predicting drug response. Histopathology using hematoxylin and eosin (H&E)-stained tissue (not genomics) remains the primary diagnostic method in cancer. Recently developed highly multiplexed tissue imaging methods promise to enhance research studies and clinical practice with precise, spatially resolved single-cell data. Here, we describe the 'Orion' platform for collecting H&E and high-plex immunofluorescence images from the same cells in a whole-slide format suitable for diagnosis. Using a retrospective cohort of 74 colorectal cancer resections, we show that immunofluorescence and H&E images provide human experts and machine learning algorithms with complementary information that can be used to generate interpretable, multiplexed image-based models predictive of progression-free survival. Combining models of immune infiltration and tumor-intrinsic features achieves a 10- to 20-fold discrimination between rapid and slow (or no) progression, demonstrating the ability of multimodal tissue imaging to generate high-performance biomarkers.
Specific Cryptosporidium antigens associate with reinfection immunity and protection from cryptosporidiosis
Authors: Carol A. Gilchrist, Joseph J. Campo, Jozelyn V. Pablo, Jennie Z. Ma, Andy Teng, Amit Oberai, Adam D. Shandling, Masud Alam, Mamun Kabir, A.S.G. Faruque, Rashidul Haque, William A. Petri
Journal: Journal of Clinical Investigation (2023)

There is no vaccine to protect from cryptosporidiosis, a leading cause of diarrhea in infants in low and middle income countries. Here we comprehensively identified parasite antigens associated with protection from reinfection. A Cryptosporidium protein microarray was constructed by in vitro transcription and translation of 1761 C. parvum, C. hominis or C. meleagridis antigens, including proteins with a signal peptide and/or a transmembrane domain. Plasma IgG and/or IgA from Bangladeshi children longitudinally followed for cryptosporidiosis from birth to three years of age, identified 233 seroreactive proteins. Seven of these were associated with protection from reinfection. These included Cp23 and Cp17, Gp900 and four additional antigens (CpSMP1, CpMuc8, CpCorA and CpCCDC1). Infection in the first year of life however often resulted in no detectable antigen-specific antibody response, and antibody responses, when detected, were (i) specific to the infecting parasite genotype, and (ii) decayed in the months post-infection. In conclusion humoral immune responses against specific parasite antigens were associated with acquired immunity. While antibody decay over time and parasite genotype-specificity may limit natural immunity, this work serves as a foundation for antigen selection for vaccine design.
Diagnostic accuracy of computer morphometry for steatosis and fibrosis assessment in patients with chronic liver disease of various etiologies
Authors: Yu.M. Stepanov, V.I. Didenko, Yu.A. Gaydar, N.Yu. Zavhorodnia, O.P. Petishko
Journal: GASTROENTEROLOGY (2023)

Background. Accurate assessment of the fibrosis stage is crucial for effective treatment. Histological examination, the primary method used for assessing liver fibrosis, has certain limitations due to variation within each stage. Computer morphometry offers an objective and quantitative approach to complement histological analysis, providing additional diagnostic information. The purpose of this study was to analyze the computer morphometry data in patients with chronic liver diseases (CLD) of different etiologies and determine their diagnostic accuracy for liver fibrosis diagnosis. Materials and methods. Seventy-five patients with CLD, namely 24 with non-alcoholic fatty liver disease (NAFLD), 8 with alcoholic liver disease (ALD), 1 with toxic hepatitis, and 42 with chronic hepatitis C (CHC), were included in the study. Percutaneous liver biopsy was performed under ultrasound guidance using a semi-automatic needle Colt Shot 16 G. The severity of fibrosis was assessed using the Metavir scale. For computer morphometry, biopsies were photographed and evaluated using the ImageJ 1.45S program (National Institutes of Health, USA). The computerized fibrosis index (CFI), steatosis index, and the number of apoptotic cells in 5 consecutive high-power fields were calculated. Receiver operating characteristic analysis was performed for CFI diagnostic accuracy assessment. Results. Advanced liver fibrosis (F3-F4) was diagnosed in 62.5 % of ALD cases and 31.0 % of CHC. The highest CFI was found in ALD, it exceeded the level of NAFLD and CHC patients by 3.3 (p &lt; 0.01) and 2 times (p &lt; 0.05), respectively. At the same time, people with NAFLD had the highest steatosis index (0.36 ± 0.11), which was 1.7 times higher (p &lt; 0.05) than in ALD and CHC. Moreover, CFI correlated with the fibrosis stage (r = 0.71, p &lt; 0.05). Stage I of liver fibrosis according to the Metavir scale is characterized by CFI up to 0.040, stage II — 0.041–0.130, stage III — 0.131–0.219, and stage IV — more than 0.220. CFI cut-off value was 0.017, which confirms the presence of liver fibrosis in patients with chronic liver diseases regardless of the etiology (sensitivity — 85.2 %, specificity — 100.0 %). Conclusions. Computer morphometry significantly improves the accuracy and reliability of histological examination, and allows to objectify morphological assessment of liver steatosis and fibrosis and to ensure long-term storage of the results.